I've seen this happen with B-factor refinement reasonably often. As I understand it the basic problem is that for small B-factors the gradient d(density)d(B) is large, but for large B-factors the gradient is small. So if the starting B-factor on an atom is very low and substantially lower than what the density supports, then the first refinement cycle can overstep to the point where there's almost no gradient, so future refinement steps don't pull it back down. Tightening the B-factor similarity restraints to surrounding atoms can help. ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Thomas, Leonard M. <lmtho...@ou.edu> Sent: 10 August 2022 17:01 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Odd Positive Density Around a Cystine
While the B value in the starting model was fine. I did drop it to a reasonable value and it now seems to be behaving, was thinking about trying that before I posted. Since this was an MR determination I did check and the starting model B value was actually smaller then the surrounding residues. I guess some thing went odd with the first round of refinement. Thank you for the suggestions. Len > On Aug 10, 2022, at 10:25 AM, Dale Tronrud <de...@daletronrud.com> wrote: > > > A large B value with positive difference density sure implies a convergence > problem with the refinement. Was the B value extreme in your starting model? > (A starting B that is wildly too large or too small at the start may cause > it to become trapped in the refinement.) Maybe if you rerun your refinement > with a moderate starting value for the B you will end up a more sensible > result. > > The only other way to end up with a parameter that directly conflicts with > the difference density is a bad restraint, but that doesn't sound likely > based on your description. > > Dale Tronrud > > On 8/10/2022 7:59 AM, Thomas, Leonard M. wrote: >> Hello All, >> I have run into something odd. In working on a structure for one of the >> groups I work with regularly, on one of the cystine residues I have a very >> large positive density peak at the sulfur position. The B value is >> approximately 4 times the other values in the residue and on other cystine >> residues. The overall structure has 2 molecules in the asymmetric unit and >> the corresponding cystine on the other monomer is behaving as I would >> expect. There are no disulfides in the structure. >> The data were collected on 9-2 at SSRL and all three of the data sets we >> collected show the same thing, all data go to about 2.2 angstroms. We are >> trying to determine the ligand binding in the molecule but this cystine is >> not involved in ligand binding. In house and other synchrotron data from >> previous protein preps and data collection runs of the same molecule grown >> in very similar condition and crystallized in the same space group have the >> residue behaving normally. >> I am open to any ideas as to what may be going on as I am rather puzzled by >> this. >> Thanks for any input, >> Len Thomas >> Leonard Thomas, Ph.D. >> Biomolecular Structure Core, Director >> Oklahoma COBRE in Structural Biology >> Price Family Foundation Institute of Structural Biology >> University of Oklahoma >> Department of Chemistry and Biochemistry >> 101 Stephenson Parkway >> Norman, OK 73019-5251 >> Office: (405)325-1126 >> lmtho...@ou.edu <mailto:lmtho...@ou.edu> >> 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